WormBase-Caltech Weekly Calls
From WormBaseWiki
Contents
- 1 Previous Years
- 2 2015 Meetings
- 2.1 September 3, 2015
- 2.1.1 Development instances at Caltech
- 2.1.2 GObA (Graph of Ontology-based Annotations)
- 2.1.3 Anatomy enrichment tool
- 2.1.4 Community allele-phenotype annotations
- 2.1.5 Logical Extensions of Gene Ontology (LEGO)
- 2.1.6 Phentoype-association file: Attributing phenotypes to genes via genetic interaction
- 2.1 September 3, 2015
Previous Years
2015 Meetings
September 3, 2015
Development instances at Caltech
- Caltech wants to provide a Beta testing environment for curators/users
GObA (Graph of Ontology-based Annotations)
- Added a couple new graph types
- Working out details before sending out to Beta testers
- Example pages:
Anatomy enrichment tool
- Enter list of genes, get a list of anatomy terms
- Developed originally by David Angeles
- Being incorporated and worked on by Raymond
Community allele-phenotype annotations
- Outreach: sending out e-mails to relevant people
- Not done yet
- May be good to travel out to labs to give instructions, outreach
- We'll gather a list of labs that publish phenotypes and contact them
- We can also push the micropublication process
Logical Extensions of Gene Ontology (LEGO)
- Further developments being made on Noctua and other LEGO software
- Lots of discussion on LEGO modeling, how to best do it
- Testing is scheduled
- Protein complexes in cellular component ontology?
- GO will collaborate with Protein Ontology group to work out how to capture that info
- Molecular function ontology annotation approach is being refactored
- Noctua being used for phenotype annotations, would be good to see how
Phentoype-association file: Attributing phenotypes to genes via genetic interaction
- Can we (and how do we) capture genes as involved in a process, for example, SynMuv genes in vulva development
- The phenotype association file currently only on direct phenotype annotations, not interaction-based phenotypes
- Gene Ontology captures these events (associations to a process, for example) with the evidence code, Inferred from Genetic Interaction